media-libs/alsa-lib:src_unpack uses eautomake instead of eautoreconf, which breaks things if the automake-generated Makefiles contain new @@-substitutions that are not placed in aclocal.m4. This can happen if Automake is not the exact same version that generated the aclocal.m4. The solution is to replace eautomake/elibtoolize with eautoreconf.
If automake is not the same version, eautomake takes care already for running eautoreconf. Don't open bugs if you don't see a failure happen and you don't know how functions work.
That was a crude answer. This is a bug reporting functionality, so (of course) my report is a bug. Otherwise I wouldn't have reported it. And no, I found no reason to check the eautomake function for a hack like that one... That said, the problem seems to be that my locally patched Automake adds some @@-subs that are not added to aclocal. And yes, that shows up as a failed ebuild, since the Automake version is still the same. Apparently, my idea of giving a general solution rather than the complete problem statement was a bad idea. Sorry for that.
That's not an hack it's a security precaution. If you use a modified automake, with the same automake version reported as official one, you're going to break more than just this.